Research workbench
Structure of S. pombe LSM2-8 with unprocessed U6 snrna
Analyse Structure of S. pombe LSM2-8 with unprocessed U6 snrna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PPN
- Type
- protein + RNA
- Length
- 1,122 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mimic of unprocessed U6 snrna; U6 snrna-associated sm-like protein LSM2; Probable U6…
- UniProt
- O94408, Q9Y7M4, O14352, O42978, Q9UUI1, O74499, O74483
- Pockets
- 9 · best druggability 0.63
Structure
x-ray diffraction · 10 distinct chains · 18% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, I | Mimic of unprocessed U6 snrna | rna | 4 | — | — |
| B | U6 snrna-associated sm-like protein LSM2 | protein | 94 | 33% helix, 37% strand | O94408 |
| C, K | Probable U6 snrna-associated sm-like protein LSM3 | protein | 75 | 11% helix, 60% strand | Q9Y7M4 |
| D, L | Probable U6 snrna-associated sm-like protein LSM4 | protein | 88 | 27% helix, 44% strand | O14352 |
| E, M | U6 snrna-associated sm-like protein LSM5 | protein | 68 | 15% helix, 57% strand | O42978 |
| F, N | U6 snrna-associated sm-like protein LSM6 | protein | 68 | 12% helix, 56% strand | Q9UUI1 |
| G | U6 snrna-associated sm-like protein LSM7 | protein | 75 | 4% helix, 56% strand | O74499 |
| H, P | U6 snrna-associated sm-like protein LSM8 | protein | 94 | 18% helix, 45% strand | O74483 |
| J | U6 snrna-associated sm-like protein LSM2 | protein | 89 | 31% helix, 39% strand | O94408 |
| O | U6 snrna-associated sm-like protein LSM7 | protein | 70 | 4% helix, 60% strand | O74499 |
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.63 | 0.74 | 66 | empty |
| 2 | 470 | 0.58 | 0.74 | 44 | empty |
| 3 | 290 | 0.54 | 0.75 | 36 | empty |
| 4 | 106 | 0.53 | 0.82 | 21 | empty |
| 5 | 116 | 0.50 | 0.80 | 22 | empty |
Interfaces
30 interfaces between chains.
- J–P · 1298 Ų buried · 15 hydrogen bonds · protein-protein
- B–H · 1280 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1145 Ų buried · 15 hydrogen bonds · protein-protein
- D–G · 1067 Ų buried · 10 hydrogen bonds · protein-protein
- J–K · 1035 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6PPN · Structure of S. pombe Lsm2-8 with unprocessed U6 snRNA · the same entry in another collection · chain J against J, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O94408
- Every structure of UniProt Q9Y7M4
- Every structure of UniProt O14352
- Every structure of UniProt O42978
- Every structure of UniProt Q9UUI1
- Every structure of UniProt O74499
- Every structure of UniProt O74483
- Elsewhere: RCSB PDB 6PPN · PDBe 6PPN · UniProt O94408 · UniProt Q9Y7M4 · UniProt O14352 · UniProt O42978 · UniProt Q9UUI1 · UniProt O74499 · UniProt O74483
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